Homolog-specific PCR primer design for profiling splice variants

Classification and review of free PCR primer design software

MOTIVATION

Polymerase chain reaction (PCR) has been a revolutionary biomedical advancement. However, for PCR to be appropriately used, one must spend a significant amount of effort on PCR primer design. Carefully designed PCR primers not only increase sensitivity and specificity, but also decrease effort spent on experimental optimization. Computer software removes the human element by performing and automating the complex and rigorous calculations required in PCR primer design. Classification and review of the available software options and their capabilities should be a valuable resource for any PCR application.

RESULTS

This article focuses on currently available free PCR primer design software and their major functions (https://pcrprimerdesign.github.io/). The software are classified according to their PCR applications, such as Sanger sequencing, reverse transcription quantitative PCR, single nucleotide polymorphism detection, splicing variant detection, methylation detection, microsatellite detection, multiplex PCR and targeted next generation sequencing, and conserved/degenerate primers to clone orthologous genes from related species, new gene family members in the same species, or to detect a group of related pathogens. Each software is summarized to provide a technical review of their capabilities and utilities.

Validation of an in vitro system to trigger changes in the gene expression of effectors of Sclerotinia sclerotiorum

AIMS

Sclerotinia sclerotiorum, the causal agent of white mold, can infect several host species, including economically important crops. In this study, we propose and validate a new in vitro system able to mimic the conditions of interaction with the host and promote the induction of S. sclerotiorum effectors.

METHODS AND RESULTS

For culture media production, we selected three plant species, common bean (Phaseolus vulgaris L, cv. Requinte.), maize (Zea mays, cv. BRS1030) and beggarticks (Bidens pilosa). To validate this system as an in vitro inducer of effectors, the qRT-PCR technique was used to investigate the expression profile of some S. sclerotiorum effector genes in each growth medium at different times after inoculation.

CONCLUSION

The results obtained in this study provide a validation of a new method to study S. sclerotiorum during mimetic interaction with different hosts. Although leaf extract does not fully represent the plant environment, the presence of plant components in the culture medium seems to induce effector genes, mimicking in planta conditions. The use of MEVM is simpler than in planta growth, bypasses problems such as the amount of mycelium produced, as well as contamination of host cells during transcriptomic and proteomic analyses.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have devised MEVM media as a model mimicking the interaction of S. sclerotiorum and its hosts and used it to evaluate in vitro expression of effectors normally expressed only in planta.

MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments

For the best results in quantitative polymerase chain reaction (qPCR) experiments, it is essential to design high-quality primers considering a multitude of constraints and the purpose of experiments. The constraints include many filtering constraints, homology test on a huge number of off-target sequences, the same constraints for batch design of primers, exon spanning, and avoiding single nucleotide polymorphism (SNP) sites. The target sequences are either in database or given as FASTA sequences, and the experiment is for amplifying either each target sequence with each corresponding primer pairs designed under the same constraints or all target sequences with a single pair of primers. Many websites have been proposed, but none of them including our previous MRPrimerW fulfilled all the above features. Here, we describe the MRPrimerW2, the update version of MRPrimerW, which fulfils all the features by maintaining the advantages of MRPrimerW in terms of the kinds and sizes of databases for valid primers and the number of search modes. To achieve it, we exploited GPU computation and a disk-based key-value store using PCIe SSD. The complete set of 3 509 244 680 valid primers of MRPrimerW2 covers 99% of nine important organisms in an exhaustive manner. Free access: http://MRPrimerW2.com.

Pan Proteome of Xanthomonas campestris pv. campestris Isolates Contrasting in Virulence

Fully sequenced genomes of Xanthomonas campestris pv. campestris (Xcc) strains are reported. However, intra-pathovar differences are still intriguing and far from clear. In this work, the contrasting virulence between two isolates of Xcc - Xcc51 (more virulent) and XccY21 (less virulent) is evaluated by determining their pan proteome profiles. The bacteria are grown in NYG and XVM1 (optimal for induction of hrp regulon) broths and collected at the max-exponential growth phase. Shotgun proteomics reveals a total of 329 proteins when Xcc isolates are grown in XVM1. A comparison of both profiles reveals 47 proteins with significant abundance fluctuations, out of which, 39 show an increased abundance in Xcc51 and are mainly involved in virulence/adaptation mechanisms, genetic information processing, and membrane receptor/iron transport systems, such as BfeA, BtuB, Cap, Clp, Dcp, FyuA, GroEs, HpaG, Tig, and OmpP6. Several differential proteins are further analyzed by qRT-PCR, which reveals a similar expression pattern to the protein abundance. The data shed light on the complex Xcc pathogenicity mechanisms and point out a set of proteins related to the higher virulence of Xcc51. This information is essential for the development of more efficient strategies aiming at the control of black rot disease.

Combining bioinformatics and conventional PCR optimization strategy for one-time design of high-specificity primers for WRKY gene family using unigene database

Gene families, like the conserved transcription factor families, evolve through gene duplications and share moderate similarity between member genes. Lack of genomic data makes it difficult to design high-specificity primers to the target genes. Furthermore, many primers under-perform in highly sensitive assays like quantitative PCR due to issues of thermodynamic nature, thereby increasing the cost and time for analysis. A methodology involving intra-species and inter-generic bioinformatic sequence comparison combined with thermodynamic estimation of primer performance was used for one-time design of gene specific primers for different WRKYs, Mitogen Activated Protein-kinases and N-methyltransferases of Coffea canephora without the aid of genome sequence resources. Out of a total 37 primer sets including 31 pairs of primers for WRKY from 34 mined WRKY Unigenes/ESTs and six pairs for genes coding for MAP kinases and NBS-LRR proteins, 32 sets exhibited high specificity of amplification upon genome analysis as well as in the high-resolution melt analysis. Furthermore, PCR optimization strategies-both in silico and experimental-indicated a superior performance of the primer sets for different applications like quantitative PCR and rapid amplification of cDNA ends. Only one set of primer resulted in mis-priming upon confirmation by DNA sequencing of the cloned amplicons. The intra-species differences and inter-generic similarities ensure high specificity of primers in all cases studied. The procedure allowed design of primers for the use in different downstream applications with high performance, specificity, yield and ease-of-use.

Validation of an in vitro system for studies of pathogenicity mechanisms in Xanthomonas campestris

Several minimal media capable of inducing pathogenicity genes have been used to study plant-pathogen interactions. An in planta assay to study a closer interaction between the bacteria and the host was also developed and has been employed by our group. In order to determine whether growth medium could be improved to better approximate in planta conditions beyond that offered by the defined minimal medium XVM1, we compared the expression of 20 Xanthomonas campestris pv. campestris (Xcc) genes by quantitative reverse transcription - polymerase chain reaction (qRT-PCR) under in vivo (bacteria recovered from the plant) and in vitro (rich medium NYG, minimal medium XVM1 and XVM1 + leaf extract) growth systems. The results showed a higher expression level of the genes in the in planta system when compared to growth in culture media. In planta growth is closest to a real interaction condition and captures the complexity of the plant cell environment; however, this system has some limitations. The main finding of our work is that the addition of plant extract to XVM1 medium results in a gene expression profile that better matches the in planta profile, when compared with the XVM1 medium alone, giving support to the use of plant extract to study pathogenicity mechanisms in Xanthomonas.

ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing

Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplification-based resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.

Gene expression of cytokeratin 19 and its molecular detection in human breast cancer cell lines

Cytokeratins have been identified as useful tools in oncology diagnostics. In this study, cytokeratin19 (CK19) expression was studied in three human breast cancer cell lines, SKBR3, BT549, and BT474 using RT-PCR. CK19 was expressed in tumor cell of different origin, showing higher expression in invasive breast cancer with ER(+) (BT474) than invasive breast cancer with ER(-) (BT549) and breast adenocarcinoma with ER(-) (SKBR3). Two primer sets were used to evaluate CK19 expression. Primer set I (hCK19/1) and primer set II (hCK19/2) were used to amplify the CK19 human gene at a 215bp and 384bp, respectively, whereas PBMC and RAW264.7 (mouse macrophage) no detectable PCR products were obtained. The sensitivity for detection was determined by two methods, i.e., cDNA dilution (the dilution of cDNA from RNA of breast cancer cells) and cell dilution (the dilution of breast cancer cells in PBMC). hCK19/2 was more sensitive than hCK19/1. In cDNA dilution, the lower limits of primer set II for detection were 400, 40 and 40 cells for SKBR3, BT549 and BT474 cells, respectively. While in cell dilution all of the 3 breast cancer cells could be detected at 1 cancer cell in 10(4), 10(6) and 10(5) PBMC, respectively. The data supported the possibility that CK19 could be detected and be the marker for breast cancer in patient blood.

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions.

Primer3--new capabilities and interfaces

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

VizPrimer: a web server for visualized PCR primer design based on known gene structure

SUMMARY

The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs).

AVAILABILITY

VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0).

CONTACT

zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.